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BioC 3.0: CHECK report for altcdfenvs on zin1

This page was generated on 2015-04-10 09:36:42 -0700 (Fri, 10 Apr 2015).

Package 35/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
altcdfenvs 2.28.0
Laurent Gautier
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/altcdfenvs
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK 

Summary

Package: altcdfenvs
Version: 2.28.0
Command: /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings altcdfenvs_2.28.0.tar.gz
StartedAt: 2015-04-09 21:29:13 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 21:31:33 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 139.8 seconds
RetCode: 0
Status:  OK 
CheckDir: altcdfenvs.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.0-bioc/R/bin/R CMD check --no-vignettes --timings altcdfenvs_2.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.0-bioc/meat/altcdfenvs.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘altcdfenvs/DESCRIPTION’ ... OK
* this is package ‘altcdfenvs’ version ‘2.28.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘Biobase’ ‘affy’ ‘makecdfenv’ ‘Biostrings’
  ‘hypergraph’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘altcdfenvs’ can be installed ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘Biostrings’ ‘hypergraph’ ‘makecdfenv’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
buildCdfEnv.biostrings: no visible global function definition for
  ‘xy2indices’
buildCdfEnv.matchprobes: no visible global function definition for
  ‘xy2indices’
copyCdfEnvAffy: no visible global function definition for ‘copyEnv’
getCdfEnvAffy: no visible global function definition for ‘getCdfInfo’
index2xy.CdfEnvAffy: no visible global function definition for
  ‘indices2xy’
matchAffyProbes : <anonymous>: no visible global function definition
  for ‘elementLengths’
matchAffyProbes: no visible global function definition for
  ‘DNAStringSet’
matchAffyProbes: no visible global function definition for ‘DNAString’
matchAffyProbes: no visible global function definition for ‘PDict’
matchAffyProbes: no visible global function definition for ‘matchPDict’
xy2index.CdfEnvAffy: no visible global function definition for
  ‘xy2indices’
toHypergraph,CdfEnvAffy : <anonymous>: no visible global function
  definition for ‘Hyperedge’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [30s/30s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
removeIndex      11.664  0.016  11.716
matchAffyProbes   7.057  0.108   7.188
CdfEnvAffy-class  5.936  0.032   6.035
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-3.0-bioc/meat/altcdfenvs.Rcheck/00check.log’
for details.

altcdfenvs.Rcheck/00install.out:

* installing *source* package ‘altcdfenvs’ ...
** R
** data
** inst
** preparing package for lazy loading
NOTE: arguments in definition for validity method for class 'AffyProbesMatch' changed from (obj) to (object)
in method for ‘toHypergraph’ with signature ‘"CdfEnvAffy"’: no definition for class “CdfEnvAffy”
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (altcdfenvs)

altcdfenvs.Rcheck/altcdfenvs-Ex.timings:

nameusersystemelapsed
AffyProbesMatch-class0.0000.0000.001
CdfEnvAffy-class5.9360.0326.035
appendCdfEnvAffy0.0080.0000.006
cdfenv0.0000.0000.001
cdfenvEx0.0040.0000.003
getxy.probeseq0.0040.0000.001
index2xy000
matchAffyProbes7.0570.1087.188
plot.CdfEnvAffy000
removeIndex11.664 0.01611.716
unique.CdfEnvAffy0.0040.0000.001
utils.FASTA0.0040.0040.008
validAffyBatch0.0000.0000.001